Development of a technology to certify engineered DNA molecules

开发验证工程 DNA 分子的技术

• 批准号: 10509988
• 负责人: Jean M Peccoud
• 金额: $ 38.8万
• 依托单位: COLORADO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-15 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10509988
• 关键词: Address; Affect; Algorithms; Architecture; Bar Codes; Biological; Biological Process; Biological Sciences; Biological Testing; Biology; Biomedical Research; Biotechnology; Blood Circulation; Cell Therapy; Certification; Clinical Research; Code; Communities; Complex; Computer Security; Computers; DNA; DNA Sequence; Data; Database Management Systems; Development; Documentation; Elements; Engineering; Ensure; Event; Fostering; Funding; Gene Expression; Generations; Genetic; Genetic Engineering; Genome engineering; Individual; Industry; Infrastructure; Knowledge; Label; Link; Methodology; Methods; Modification; Molecular; Mutate; Mutation; Names; Persons; Pharmaceutical Preparations; Plasmids; Play; Production; Property; Publications; Recombinants; Recording of previous events; Records; Reproducibility; Research; Resources; Role; Safety; Scheme; Scientist; Secure; Security; Signal Transduction; Software Engineering; Standardization; System; Technology; Testing; Therapeutic; Tube; United States National Institutes of Health; Validation; Variant; Visualization software; Writing; base; bioinformatics pipeline; biological research; computer network; cryptography; design; digital; engineering design; expression vector; follow-up; gene therapy; genetic element; improved; innovation; medical specialties; new technology; online resource; research and development; response; technology validation; therapeutic protein; tool; vaccine development; web site

PROJECT SUMMARY The open availability of authenticated, well-documented research materials is essential for scientific progress. Plasmids have become essential research tools to address almost any question in biology, and together with other forms of engineered DNA molecules, are essential for clinical research applications including gene therapy, vaccine development, and the production of recombinant drugs. Currently, the two common links between a plasmid and its documentation are the plasmid names and the plasmid sequence. Despite the central role that plasmids play in biomedical research and development, there is no guaranteed way to connect a physical plasmid in a tube to its documentation. A pipetting error, a labelling error, a spontaneous mutation, or an undocumented modification of the plasmid are some of the events that could result in a tube containing a different plasmid than what is indicated on the label. In addition, there is no standardized, secure approach to documenting the sequence, function, and lineage of a plasmid. As a result, there are widespread discrepancies between the physical sequences of the plasmids in circulation in the life science community and their supposed reference sequence. This situation creates reproducibility issues, slows down R&D efforts and raises significant security and safety issues for biotechnology applications. We are proposing to develop a new digital certificate technology, enabled by a web-based resource called MyPlasmid.org, that will provide a robust, physical link between engineered DNA molecules, their electronic documentation, and their authors. This technology will produce unique DNA sequences generated by cryptographic algorithms that can be inserted into an engineered DNA molecule. MyPlasmid.org will allow users to document their genetic designs by aggregating the documentation of individual genetic elements as well as combinations of elements. In addition, it will link the computer records of the engineered DNA sequence directly to the molecule itself and provide a method to retrieve documentation without a priori knowledge of the plasmid's identity. Short unique DNA sequences called certificates will be inserted between the functional blocks of engineered sequences. Unlike DNA barcodes, certificates will be computed by cryptographic algorithms using the DNA sequence itself and the author's identity as input so that users of engineered DNA molecules can verify the origin and integrity of certified DNA molecules. The technology described in this proposal is expected to foster a transition similar what has been observed in the semi-conductor industry where different stakeholders invest in the development of circuits that can be easily combined in larger designs that can then be manufactured by foundries not involved in the chip design. By ensuring that the sequence, origin, function, and lineage of engineered DNA molecules is accurately tracked and conveyed to all users, the proposed technology will improve the reproducibility, utility, and potential application of engineered DNA molecules in the life sciences.

项目摘要 公开提供经过认证的、有据可查的研究材料对科学进步至关重要。 质粒已成为解决生物学中几乎所有问题的基本研究工具， 其它形式的工程DNA分子，对于临床研究应用包括基因治疗， 疫苗开发和重组药物的生产。目前，两个共同的链接之间的一个 质粒及其文档是质粒名称和质粒序列。尽管它的核心作用是 质粒在生物医学研究和开发中发挥作用，没有保证的方法将物理连接到 质粒在一个管到它的文档。移液错误、标记错误、自发突变或 质粒的未记录的修饰是一些可能导致含有不同的 比标签上显示的要多。此外，没有标准化的安全方法来 记录质粒的序列、功能和谱系。因此， 在生命科学界循环的质粒的物理序列和它们的假设序列之间， 参考序列这种情况造成了可重复性问题，减缓了研发工作，并提高了生产效率。 生物技术应用的安全问题。 我们建议发展一项新的数码证书技术，并透过网上资源， MyPlasmid.org，这将提供一个强大的，工程DNA分子之间的物理联系，他们的电子 文档及其作者。这项技术将产生独特的DNA序列， 密码算法，可以插入到一个工程DNA分子。MyPlasmid.org将允许用户 通过汇总单个遗传元素的文件来记录它们的遗传设计， 元素的组合。此外，它将直接连接工程DNA序列的计算机记录 并提供了一种方法来检索文档，而无需质粒的先验知识。 身份称为证书的短的独特DNA序列将被插入功能块之间 工程序列。与DNA条形码不同，证书将通过使用 DNA序列本身和作者的身份作为输入，以便工程DNA分子的用户可以验证 DNA分子的来源和完整性该提案中描述的技术预计将 促进类似于在半导体行业中观察到的过渡， 投资于电路的开发，这些电路可以很容易地组合成更大的设计，然后可以制造 由不参与芯片设计的代工厂生产。通过确保基因的序列、起源、功能和谱系 工程DNA分子被准确地跟踪并传达给所有用户，所提出的技术将 提高工程DNA分子在生命科学中的再现性、实用性和潜在应用。